mysql> select tableName from trackDb_wigExample; ......... .......... | zhaoLabRestingNucleosomeRevWig | | zhaoLabRestingUnphosPolII | | zhaoLabRestingUnphosPolIIBedGraph | +------------------------------------------------------------------+ 4374 rows in set (0.01 sec)
I opened our website http://research.icts.uiowa.edu/genomebrowser/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on looks like nothing changed. Where should I look for Apache error logs on EL5? Thanks, Tiandao On Thu, May 6, 2010 at 12:11 PM, Hiram Clawson <[email protected]> wrote: > Good Morning Tiandao: > > What do you see if you dump the contents of your trackDb_wigExample table: > > mysql> select tableName from trackDb_wigExample; > > While viewing your genome browser where you expect the track to appear, > take a look at your Apache error logs to see if there are any unusual > errors being printed out. > > When viewing your genome browser, add this variable JKSQL_TRACE=on to the > URL in > your WEB browser address: > http://your.domain.com/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on > > Take a look at your Apache error log and see if there are any SQL > operations > begin performed with your trackDb_wigExample table. > > --Hiram > > Tiandao Li wrote: > >> Hi, >> >> We installed a local genome browser with minimal installation. I tried to >> load wig files to local database. >> >> First, use wigEncode to make wig/wib files. >> >> l...@test01:~$ wigEncode PolII_eland_sorted2.wig PolII.wig PolII.wib >> Converted PolII_eland_sorted2.wig, upper limit 4385.00, lower limit 2.00 >> >> 2. mkdir wib folder inside of /mnt/nfs/genomdata/gbdb/hg18/ >> >> 3. [l...@research ~]$ /opt/kent/hgLoadWiggle >> -pathPrefix=/mnt/nfs/genomdata/gbdb/hg18/wib hg18 wigExample PolII.wig >> Connected to database hg18 for track wigExample >> Creating wiggle table definition in hg18.wigExample >> Saving wiggle.tab >> WARNING: Exceeded chrM size 16624 > 16571. dropping 3 data point(s) >> Loading hg18 >> >> 4. [l...@research ~]$ cp PolII.wib /mnt/nfs/genomdata/gbdb/hg18/wib/ >> >> 5. [l...@research trackDb]$ cd bin/kent/src/hg/makeDb/trackDb >> [l...@research trackDb]$ /opt/kent/hgTrackDb human hg18 >> trackDb_wigExample >> ../../lib/trackDb.sql . >> .... >> .... >> Loaded 4374 track descriptions total >> Loaded database hg18 >> >> 6. [l...@research trackDb]$ /opt/kent/hgFindSpec human hg18 >> hgFindspec_wigExample ../../lib/hgFindSpec.sql . >> found include file: ./human/hg18/trackDb.chainNet.ra >> found include file: ./human/hg18/trackDb.encode.ra >> found include file: ./human/hg18/trackDb.encodeGenes.ra >> found include file: ./human/hg18/trackDb.encodeTxLevels.ra >> found include file: ./human/hg18/trackDb.encodeChip.ra >> found include file: ./human/hg18/trackDb.encodeChrom.ra >> found include file: ./human/hg18/trackDb.encodeCompAndVar.ra >> found include file: ./human/hg18/trackDb.wgEncode.ra >> found include file: ./human/hg18/wgEncodeRikenCage.alpha.ra >> found include file: ./human/hg18/wgEncodeRikenCage.beta.ra >> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.alpha.ra >> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.beta.ra >> found include file: ./human/hg18/wgEncodeGisPet.alpha.ra >> found include file: ./human/trackDb.encode.ra >> found include file: ./human/trackDb.chainNet.ra >> found include file: ./trackDb.chainNet.ra >> Loaded 216 search specs total >> Loaded database hg18 >> >> 7. [l...@research trackDb]$ locate hg.conf >> /var/www/html/genomebrowser/cgi-bin/hg.conf >> >> vim /var/www/html/genomebrowser/cgi-bin/hg.conf >> >> change db.trackDb to >> >> db.trackDb=trackDb_wigExample,trackDb >> >> Now, I open local genome browser, still can't see my wigExample file. >> >> mysql> show tables; >> | wigExample | >> | xenoEst | >> | xenoMrna | >> | xenoRefFlat | >> | xenoRefGene | >> | xenoRefSeqAli | >> | yaleBertoneTars | >> +------------------------------------------------------------------+ >> >> mysql> select tableName from trackDb; >> >> | wgEncodeYaleChIPseqViewPeaks | >> | wgEncodeYaleChIPseqViewSignal | >> | wgRna | >> | xenoEst | >> | xenoMrna | >> | xenoRefGene | >> | yaleBertoneTars | >> +------------------------------------------------------------------+ >> >> Any help appreciate!!! >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
